From owner-chemistry@ccl.net Fri Oct 24 09:32:01 2008 From: "Martin Bohl martin^^moldiscovery.com" To: CCL Subject: CCL: Release of MetaSite 3.0 software for Site of Metabolism prediction Message-Id: <-37975-081024093013-26327-rd8ELvMq2lQkuN0FHuevVQ(~)server.ccl.net> X-Original-From: "Martin Bohl" Date: Fri, 24 Oct 2008 09:30:09 -0400 Sent to CCL by: "Martin Bohl" [martin^moldiscovery.com] Dear Colleagues, We would like to draw your attention to MetaSite 3.0 software for Site of Metabolism prediction and Metabolite Enumeration. Optimizing metabolic stability and metabolite profiling are key elements in understanding bioavailability, elimination, and toxicity, hence are critical for drug discovery. Experimental determination requires considerable material and is resource demanding, meaning that it tends to happen later in the discovery process. This means that much time can be spent optimizing a lead compound, only to have serious problems with metabolism. MetaSite 3.0 facilitates these tasks for Cytochrome-mediated metabolism in silico, meaning that metabolism problems can be addressed earlier in the process, in tandem with addressing potency and selectivity. Once the Site of Metabolism is known, stability can be increased through chemical modification at the site. This can be problematic if (a) the site is key for potency or selectivity or (b) direct blocking may result in complete inhibition of the cytochrome leading to toxicity problems. In addition to predicting the Site of Metabolism, MetaSite 3.0 also predicts the functionality that is directing the site of metabolism, hence providing an alternative modification site. MetaSite 3.0 also predicts the most likely metabolites, and coupled with exact mass and relative retention time prediction speeds up experimental analysis. The method is training-set independent and is based on spatial recognition using GRID Molecular Interaction Fields, in combination with chemical reactivity and reaction mechanism propensity, leading to robust predictivity (~85% accuracy within the top 3 predictions). More information is available in the publication: J. Med. Chem., 48, 6970-6979 (2005) (http://dx.doi.org/10.1021/jm050529c). MetaSite is the only software developed using experimental information > from the human CYP Consortium Initiative, a joint venture between pharmaceutical companies and Molecular Discovery, working together to solve the most important issues in drug metabolism (for further information on CYP Consortium Initiative, see http://www.moldiscovery.com/consortia/CYP). More information about MetaSite 3.0 can be found here: http://www.moldiscovery.com/soft_metasite.php Kind regards, Martin Dr Martin Bohl Commercial Director Molecular Discovery Ltd Email: martin[at]moldiscovery[dot]com Molecular Discovery provides robust, high-quality and innovative computational methods addressing pharmaceutical needs in the fields of chemoinformatics, ADME and metabolism research. Other Molecular Discovery software products offer calculation of accurate Molecular Interaction Fields (GRID), building of predictive models using unique ADME/Tox descriptors (VolSurf), scaffold hopping (SHOP), pKa prediction (MoKa) and general 3D-QSAR modeling (Almond) to improve efficiency in modern drug discovery. More information can be found on the main page: http://www.moldiscovery.com/ From owner-chemistry@ccl.net Fri Oct 24 10:07:00 2008 From: "sobereva sobjubao[#]yahoo.com.cn" To: CCL Subject: CCL:G: Gaussian 03W for Windows Message-Id: <-37976-081024065002-31037-OaNUsghC+lbx22azQCy8RQ~!~server.ccl.net> X-Original-From: sobereva Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 24 Oct 2008 02:49:40 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: sobereva [sobjubao{=}yahoo.com.cn] Hi, D.01 or later version of G03W is what you need. It support SMP,you can simply add "nproc=4" to route section. CPU usage will nearly reach 100% at most time(except for some subprograms don't support parallel calculation). --Lu Tian --- "Carmela Bonaccorso bonaccorsoc%gmail.com" wrote: > > Sent to CCL by: "Carmela Bonaccorso" [bonaccorsoc > ~~ gmail.com] > Hello > > I'm a beginner in the field of Computational > Chemistry. > I would like to know what version of Gaussian 03 > should I use on a machine with the following cpu: > INTEL CORE 2 QUAD Q8200. I need the Parallel > version: Single multiprocessor machine license or > the Serial (Single CPU) Version: Single Windows > machine license? > Now I'm working with Gaussian 03 Rev.B03 and obtain > olny 25% of cpu usage on the quad core machine and > 50% on a dual core machine and never reached 100%. > I have no problem of Ram or disk space... > The problem is related to the older version that I'm > using or I neglect some Link0 commands? (I usually > specify only nprocshared=4) > Thanks a lot. > > Bonaccorso Carmela > University of Catania > bonaccorsoc###gmail.com > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the *_* > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST*_*ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ > > > From owner-chemistry@ccl.net Fri Oct 24 12:19:01 2008 From: "Mark Rewt mark.rewt###gmail.com" To: CCL Subject: CCL: Where to find drug half life prediction software Message-Id: <-37977-081024110042-1012-oed03qRzXpEKAJbloTv9fg^^server.ccl.net> X-Original-From: "Mark Rewt" Content-Type: multipart/alternative; boundary="----=_Part_49752_24790019.1224860430856" Date: Fri, 24 Oct 2008 19:00:29 +0400 MIME-Version: 1.0 Sent to CCL by: "Mark Rewt" [mark.rewt{:}gmail.com] ------=_Part_49752_24790019.1224860430856 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all, Please help to find Drug half life prediction software. Mark ------=_Part_49752_24790019.1224860430856 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all,

Please help to find Drug half life prediction software.


Mark

------=_Part_49752_24790019.1224860430856-- From owner-chemistry@ccl.net Fri Oct 24 15:30:00 2008 From: "nadia boutabba n_boutabba__yahoo.fr" To: CCL Subject: CCL:G: global minimum Message-Id: <-37978-081024114358-10120-yFp4oqOFGPa1RbDFWoey0A#,#server.ccl.net> X-Original-From: "nadia boutabba" Date: Fri, 24 Oct 2008 11:43:55 -0400 Sent to CCL by: "nadia boutabba" [n_boutabba|,|yahoo.fr] Dear ccl members, i optimize a small molecule, i need to calculate its dissociation energy by different dft method how to obtain a minimum? i would say how to be sure that i have a minimum.after the optimization i calculated the freq job and all frequencies are real, in low frequencies there is six near zero. may be i need the global minimum of the molecule, i see in the ccl forum that this is possible by applying the simulated annealing method ( deterministic for small molecule). but i did not find any input gaussian example dealing with this? any help? thank you very much